loci.formats.in
Class ICSReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.in.ICSReader

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.StatusReporter

public class ICSReader
extends loci.formats.FormatReader

ICSReader is the file format reader for ICS (Image Cytometry Standard) files. More information on ICS can be found at http://libics.sourceforge.net

Source code:

Trac, SVN

Author:

Melissa Linkert linkert at wisc.edu

Field Summary

protected int	bitsPerPixel Number of bits per pixel.
protected String	currentIcsId Current filename.
protected String	currentIdsId
protected byte[]	data Image data.
protected loci.formats.Location	icsIn Current ICS file.
protected boolean	versionTwo Flag indicating whether current file is v2.0.

Fields inherited from class loci.formats.FormatReader

collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

currentId, debug, debugLevel, format, statusListeners, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

ICSReader()
Constructs a new ICSReader.

Method Summary

void	close()
int	fileGroupOption(String id)
String[]	getUsedFiles()
protected void	initFile(String id)
boolean	isThisType(byte[] block)
byte[]	openBytes(int no, byte[] buf)

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, close, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries

Methods inherited from class loci.formats.FormatHandler

addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getSuffixes, isThisType, isThisType, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

Field Detail

currentIcsId

protected String currentIcsId

Current filename.

currentIdsId

protected String currentIdsId

icsIn

protected loci.formats.Location icsIn

Current ICS file.

bitsPerPixel

protected int bitsPerPixel

Number of bits per pixel.

versionTwo

protected boolean versionTwo

Flag indicating whether current file is v2.0.

data

protected byte[] data

Image data.

Constructor Detail

ICSReader

public ICSReader()

Constructs a new ICSReader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

fileGroupOption

public int fileGroupOption(String id)
                    throws loci.formats.FormatException,
                           IOException

Specified by:

fileGroupOption in interface loci.formats.IFormatReader

Overrides:

fileGroupOption in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws loci.formats.FormatException,
                        IOException

Throws:

loci.formats.FormatException

IOException

getUsedFiles

public String[] getUsedFiles()

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.FormatReader

close

public void close()
           throws IOException

Specified by:

close in interface loci.formats.IFormatHandler

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
                        IOException

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException